Nalin Goonesekere, Ph.D. Assistant Professor Department of Chemistry and Biochemistry University of Northern Iowa Cedar Falls, IA 50614-0423 Office: 283 McCollum Science Hall Voice: (319) 273-3949 Fax: (319) 273-7127 E-mail: nalin.goonesekere@uni.edu Area Biochemistry, Bioinformatics, Structural Biology Degrees B.Sc. University of Colombo, Sri Lanka. Ph.D. Princeton University. Research Interests The end of the 20th century can be characterized as a golden era in biochemistry, as much as the dawn of the 20th century was for physics, since it set the stage for the complete sequencing of the Human Genome and other important mammalian and microbial genomes. This monumental effort has so far revealed the genetic ‘blueprint' of over 300 organisms. An important scientific challenge for the 21st century is the interpretation of the vast amounts of DNA sequence data which comprise a genome, in order to provide tangible benefits to humankind - whether it be new protein targets for drugs, or perhaps more efficient enzymes for use in biotechnology. A major step in such an endeavor is the identification and characterization of proteins encoded by a genome. Since experimental characterization of all proteins in an organism is not feasible at present, computer algorithms are used to provide an initial annotation. Though significant progress has been made in this field of bioinformatics, there is much work yet to be done. For example, current bioinformatics tools fail to detect homologs for nearly 50% of all proteins predicted from various genomes. Thus, there is no information about the structure or function of these proteins, or their role in each organism. Our research interests fall into two broad categories: Development of Bioinformatic Tools In the past few years, We have been improving the most popular bioinformatics tool that is currently available, BLAST (Nucleic Acids Research, 25 17 3389). We have been using our expertise in structural biology to incorporate protein structure data into BLAST, to significantly enhance its capability in annotating proteins through detection of homologs. We have now incorporated a context-specific amino acid substitution matrix (Protein Science, 12 Suppliment 2 546) into BLAST, creating CSSM-BLAST (manuscript in preparation). We have also obtained a probability distribution of gaps that in proteins and have shown that quite intriguingly, it demonstrates a distinct bi-linear character (Nucleic Acids Research, 32 9 2838). One of our research projects is to develop a secondary structure specific gap penalty function based on this data. As a subsequent step, we wish to incorporate this function into CSSM-BLAST. We are also pursuing our interests in developing structure-based amino acid substitution matrices. Structural and Functional Annotation of Protein Sequences Our second area of interest is in using bioinformatics tools developed by us, and others, to provide structural and functional annotation of genomic protein sequences identified through experimental study. Collaborative Research Projects 1. Provide structural annotation to a protein that is associated with the nuclear pore complex, REA1 (Dr. R. Dhar and colleagues from the National Cancer Institute). 2. Isolation of disease resistance genes (R genes) conferring resistance to the fungus Fusarium verticillioides in corn (Dr. James Jurgenson of the Department of Biology). 3. Transcriptional profiling of drought tolerance of the reproductive structure s of barley (Dr. Tilahun Abebe of the Department of Biology). Selected Publications 1. Schutt, C.E., Myslik, J.C., Rozycki, M.D., Goonesekere, N.C.W. and Lindberg, U. (1993) The Structure of profilin:actin at 2.55 angstrom resolution Nature 365 810. 2. Zeppezauer, E. S. C., Goonesekere, N.C.W., Rozycki, M.D., Myslik, J.C., Dauter, Z., Lindberg, U. and Schutt, C.E. (1994) The structure of profilin at 2.0 angstrom resolution J. Mol. Biol. 240 459. 3. *Goonesekere, N.C.W., Gunasekera, M.B. and Fernandopulle, N. (1999) Use of DNA typing For Criminal Casework in Sri Lanka. Proceedings of the 10th International Symposium on Human Identification Promega Corporation,Wisconsin, U.S.A.. 4. *Tiedemann, R., Kurt, F., Goonesekere, N.C.W., Gunasekera, M.B., and Ratnasooriya, W.D. (1999) A simulation study on the viability of Sri Lankan elephant populations. Folia Zoologica 48 (supp. 1): 95-104. 5. *Fernandopulle, N., Gunasekera, M.B. and Goonesekere, N.C.W. (2002) Population genetics of eight STR loci from Sri Lanka. Forensic Science International 126 1 93. 6. *Vandebona, H., Goonesekere, N.C.W., Ratnasooriya, W.D., Alahakoon, J. and Gunasekera, M.B. (in press) The establishment of paternity of elephants born in captivity in Pinnawela Elephant Orphanage, Sri Lanka, by DNA fingerprinting (2002). International Zoo Yearbook 39. 7. *Vandebona, H., Goonesekere, N.C.W., Tiedemann, R., Ratnasooriya, W.D., and Gunasekera, M.B. (2002) Sequence variation at two mitochondrial genes in the Asian elephant (Elephas maximus) population in Sri Lanka. Mammalian Biology 67 4 193. 8. *Mapatuna, Y., Gunasekera, M.B., Ratnasooriya W.D., Goonesekere, N.C.W. & Bates P.J.J. (2002) Unravelling the taxonomic status of the Genus Cynopterus (Chiroptera:Pteropodidae) in Sri Lanka by multivariate morphometrics and mitochondrial DNA sequence analysis Mammalian Biology 67: 321. 9. Goonesekere, N.C.W. and Lee B. (2003) Context specific substitution matrices for the detection of structural homologs. Protein Science, Vol 12 Supplement 2 546 10. Goonesekere, N.C.W. and Lee B. (2004) Frequency of gaps observed in a structurally aligned protein pair database suggest a simple gap penalty function Nucleic Acids Research 32 9 2838. Edit your personal information